SASDUU5

Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 bound to 3'UTR fragment of ADP-ribosylation factor 1

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2025-01-14T14:00:42.258741+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 bound to 3'UTR fragment of ADP-ribosylation factor 1

Concentration— – 4.0 Buffer / pH50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol / 7.0
Experimental temperature4.0 Facility / beamlineCEITEC / Rigaku BioSAXS-1000
Wavelength0.154 nmExposure3600.0 s × 1

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177)
View sequence
GSHMEENLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPMVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGHVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC
proteinHomo sapiensO95793178–577dimerMolecule count 244.387 kDa
3'UTR fragment of ADP-ribosylation factor 1
View sequence
GGAGUGCCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGGUACUCC
RNAHomo sapiens——–—monomerMolecule count 114.185 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1475[3]0.00919616–0.400793 1/AHas uncertainty columnMissing 08sasbdb/entries/u5/sasduu5/source/SASDUU5.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)13.38—Å
i0Guinier0.798389—arbitrary
i0P(r)0.7547—arbitrary
mwExperimental94.2—kDa
mwPorod80.6—kDa
porod_volumePorod129.0—ų
rgGuinier4.9080.886Å
rgP(r)4.62—Å

These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.

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3. Source Fits and Models Source Fits & Models

Fit 1 · CORAL ATSAS 2.8.4 (r10552)

χ²: 0.96CorMap p: 0.055Unit: 1/A
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—mixCORAL ATSAS 2.8.4 (r10552)—101.6—Model Image
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4. Source File Index Source Files

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5. Experiment Description and Publication Experiment & Publication

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6. Complete Source Record Complete Source Record

The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.

Open the original SASBDB entry

Buffer and Sample Properties

Buffer name50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanolBuffer concentration—
pH7.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2020-05-04Storage / measurement temperature4.0 / 4.0
Exposure time3600.0Frames1
Wavelength0.154Sample-to-detector distance0.48
SourceX-ray in houseDetectorPilatus 100K
Facility / beamlineCEITEC / Rigaku BioSAXS-1000 · Brno, Czech Republic
q range0.092 – 4.008Sample volume / flow rate100.0 / 0.6

Original SASBDB Plots

Experimental I(q)
Experimental I(q)
Experimental I(q), log-log
Experimental I(q), log-log
Guinier plot
Guinier plot
Kratky plot
Kratky plot
P(r) plot
P(r) plot

Downloadable Files

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full_entry_zip:source record and ZIP contents (4 items)
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All source fields (unfiltered)

Every source field is expanded here, including empty values, list members and fields already shown above.

summary.json:173 field values
Field pathRaw value
codeSASDUU5
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleA Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy.
project.publication.titleA Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy.
project.publication.author_listTripepi A, Shakoor H, Klapetek P
project.publication.journalCurr Protoc
project.publication.doi10.1002/cpz1.70084
project.publication.pmid39781608
project.publication.published_date2025 Jan
project.statusreleased
project.submitted_date2024-03-22
project.released_date2025-01-14
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDUU5.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDUU5.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUU5_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUU5_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUU5_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUU5_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDUU5.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 100K
experiment.instrument.detector.resolution172.0
experiment.instrument.nameCEITEC
experiment.instrument.cityBrno
experiment.instrument.countryCzech Republic
experiment.instrument.beamline_nameRigaku BioSAXS-1000
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray in house
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameDouble-stranded RNA-binding protein Staufen homolog 1 (Δ1-177)
experiment.sample.molecule[0].short_nameStau1_dsRBD3-end
experiment.sample.molecule[0].sequenceGSHMEENLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPMVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGHVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeO95793
experiment.sample.molecule[0].uniprot_range_first178
experiment.sample.molecule[0].uniprot_range_last577
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS ITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF PVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN LNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN AAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE KEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ PTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM VPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH VPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES CHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC
experiment.sample.molecule[0].mw44.387
experiment.sample.molecule[0].total_mw88.774
experiment.sample.molecule[0].number_molecules2
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionDouble-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2. The protein construct used for SAXS contains four additional non-native amino acids at the N-terminus (GSHM).
experiment.sample.molecule[1].long_name3'UTR fragment of ADP-ribosylation factor 1
experiment.sample.molecule[1].short_nameARF1
experiment.sample.molecule[1].sequenceGGAGUGCCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGGUACUCC
experiment.sample.molecule[1].organismHomo sapiens
experiment.sample.molecule[1].uniprot_codenull
experiment.sample.molecule[1].uniprot_range_firstnull
experiment.sample.molecule[1].uniprot_range_lastnull
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeRNA
experiment.sample.molecule[1].uniprot_sequence
experiment.sample.molecule[1].mw14.185
experiment.sample.molecule[1].total_mw14.185
experiment.sample.molecule[1].number_molecules1
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_description
experiment.sample.buffer.name50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameHuman Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 bound to 3'UTR fragment of ADP-ribosylation factor 1
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressnull
experiment.contributor[0].affiliation[0].full_nameCEITEC - Central European Institute of Technology, Masaryk University
experiment.contributor[0].affiliation[0].webpagehttps://www.ceitec.eu/
experiment.contributor[0].contributor_nameTomas
experiment.contributor[0].contributor_surnameKlumpler
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2020-05-04
experiment.storage_temperature4.0
experiment.cell_temperature4.0
experiment.exposure_time3600.0
experiment.number_of_frames1
experiment.wavelength0.154
experiment.sample_detector_distance0.48
experiment.concentration_minnull
experiment.concentration_max4.0
experiment.sample_volume100.0
experiment.flow_rate0.6
experiment.s_min0.092
experiment.s_max4.008
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDUU5_fit1_model1_img.png
fits[0].models[0].softwareCORAL
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelmix
fits[0].models[0].software_versionATSAS 2.8.4 (r10552)
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fits[0].models[0].model_mw101.6
fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user195
fits[0].fit_unit1/A
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fits[0].softwareCORAL
fits[0].chi_square_value0.96
fits[0].p_value0.055
fits[0].fit_residual_plotSASDUU5_fit1_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDUU5_fit1.fit
fits[0].fit_loghttps://www.sasbdb.org/media/fitting_files/log_files/coral1_RfJ14E4.log
fits[0].software_versionATSAS 2.8.4 (r10552)
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSAXS data from solutions of double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 bound to the 3'UTR fragment of ADP-ribosylation factor 1 in 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH 7 were collected using a Rigaku BioSAXS-1000 instrument at CEITEC (Brno, Czech Republic) equipped with a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.00 mg/ml was measured at 4°C. One 3600 second frame was collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.
tags[]
intensity_unitarbitrary
experimental_mw94.2
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw80.6
porod_mw_errornull
pddf_i00.7547
pddf_i0_errornull
guinier_i00.798389
guinier_i0_errornull
pddf_rg4.62
pddf_rg_errornull
guinier_rg4.908
guinier_rg_error0.886
pddf_dmax13.38
pddf_dmax_errornull
porod_volume129.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last21
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDUU5_datloglog_img.png
symmetrynull
last_modified2025-01-14T14:00:42.258741+01:00
bragg_peak[]
manifest.json:34 field values
Field pathRaw value
codeSASDUU5
statussuccess
started_at2026-08-11T16:25:50.866151+00:00
finished_at2026-08-11T16:25:58.658902+00:00
source_last_modified2025-01-14T14:00:42.258741+01:00
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View the complete summary.json source
{
  "code": "SASDUU5",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy.",
    "publication": {
      "title": "A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy.",
      "author_list": "Tripepi A, Shakoor H, Klapetek P",
      "journal": "Curr Protoc",
      "doi": "10.1002/cpz1.70084",
      "pmid": "39781608",
      "published_date": "2025 Jan"
    },
    "status": "released",
    "submitted_date": "2024-03-22",
    "released_date": "2025-01-14"
  },
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  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUU5_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUU5_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUU5_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUU5.sascif",
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      "beam_geometry": "",
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      "point_source": null,
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177)",
          "short_name": "Stau1_dsRBD3-end",
          "sequence": "GSHMEENLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPMVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGHVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC",
          "organism": "Homo sapiens",
          "uniprot_code": "O95793",
          "uniprot_range_first": 178,
          "uniprot_range_last": 577,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS\nITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF\nPVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN\nLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN\nAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE\nKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ\nPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM\nVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH\nVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES\nCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC",
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          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2. The protein construct used for SAXS contains four additional non-native amino acids at the N-terminus (GSHM)."
        },
        {
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          "short_name": "ARF1",
          "sequence": "GGAGUGCCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGGUACUCC",
          "organism": "Homo sapiens",
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "RNA",
          "uniprot_sequence": "",
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          "total_mw": 14.185,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": ""
        }
      ],
      "buffer": {
        "name": "50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 bound to 3'UTR fragment of ADP-ribosylation factor 1",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": null,
            "full_name": "CEITEC - Central European Institute of Technology, Masaryk University",
            "webpage": "https://www.ceitec.eu/"
          }
        ],
        "contributor_name": "Tomas",
        "contributor_surname": "Klumpler",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2020-05-04",
    "storage_temperature": 4.0,
    "cell_temperature": 4.0,
    "exposure_time": 3600.0,
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    "wavelength": 0.154,
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    "concentration_min": null,
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    "seccolumn": null
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      "software": "CORAL",
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      "fit_residual_plot": "SASDUU5_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUU5_fit1.fit",
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDUU5_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2025-01-14T14:00:42.258741+01:00",
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}
View the complete manifest.json source
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